I am going to show you something fairly technical which will teach you about hidden files.
If you dont want to do it, or dont understand it, then fine, but others may find it useful.
Go to your Windows start menu and select the Run option.
In the Run window type Cmd and press OK
A small black Window will open with the name of a directory like C:\Documents and Settings\.......
Next to the flashing cursor type CD\ and press enter
The directory will now show C:\>
This is your C root directory
Type DIR and press enter to list all your files in the root
I get 2 files (AUTOEXEC.BAT and CONFIG.SYS plus three folders)
Now type attrib *.* and press enter (that is "attrib", space, asterisk, full stop, asterisk
This is showing you all the attributes of the files in your root.
Note there are files called boot.ini, io.sys. msdos.sys and so on.
But none of these files appeared when you typed DIR.
Well if you look to the LEFT of the files there is a H.
This is saying they are hidden files, the S is saying they are system files.
Note the only two that appeared when you did DIR were the 2 WITHOUT the H against them.
THESE ARE VERY IMPORANT WINDOW FILES. NEVER TOUCH THEM OR YOUR WINDOWS WILL STOP WORKING.
So as you can see, there are all sorts of hidden files in Windows and if you dont copy them across to your external drive your Windows sysytem will never work when you come to restore.
Again, a clone or copy of the disk will pick up all these important hidden Windows files which is why it is best to do a clone.